RNA secondary structure analysis often requires searching for potential helices in
large sequence data. We present a utility program that efficiently locates potential
helical regions under RNA base pairing rules, which include Watson-Crick as well as G-U
pairs. It accepts a target and a query set of sequences, and determines all exact
matches under RNA rules between target and query sequences that exceed a specified
length.

If you need to create larger output than we permit for online use, or want to
incorporate into your own pipeline, please download the program from the BiBiServ
download department.